Kondrashov, A.S. and M. Shpak. 1998. On the origin of species by means of assortative mating. Proceedings of the Royal Society of London B, 265: 2273-2278

Shpak, M. and A.S. Kondrashov. 1999. Applicability of the hypergeometric model to haploid and diploid phenotypic traits. Evolution, 53: 600-604.

Shpak, M. and G.P. Wagner. 2000. Asymmetry of configuration spaces induced by unequal crossover. Artificial Life 6: 25-43.

Barton, N.H. and M. Shpak. 2000. The effects of epistasis on the shape of multilocus clines Genetical Research, 75: 175-198.

Barton, N.H. and M. Shpak. 2000. Stability of symmetrical solutions to polygenic models. Theoretical Population Biology 57: 249-263.

Shpak, M. and G.A. Churchill. 2000. The information content of a character under a Markov model of evolution. Molecular Phylogenetics and Evolution 17: 231-243.

Shpak, M. and K. Atteson 2002. A survey of unequal crossover systems and their mathematical properties. Bulletin of Mathematical Biology 64: 703-746.

Stadler, B.M.R., P.F. Stadler, M. Shpak, and G.P. Wagner. 2002. Recombination spaces, metrics, and pretopologies. Zeitschrift fur Physikalische Chemie 216: 217-234.

Shpak, M., P.F. Stadler, G.P. Wagner, and J. Hermisson. 2004. Aggregation of variables and system decomposition: application to fitness landscape analysis. Theory in Biosciences 123: 33-68.

Shpak, M., P.F. Stadler, G.P. Wagner, and L. Altenberg. 2004. Simon-Ando decomposability and mutation-selection dynamics. Theory in Biosciences 123: 139-180.

Shpak, M. 2005. The role of deleterious mutations in allopatric speciation. Evolution 59: 1389-1399.

Shpak, M. 2005. The evolution of variance in offspring number: the effect of population size and migration. Theory in Biosciences 124: 65-85.

Shpak, M. and S. Gavrilets. 2006. Population genetics: multilocus. Nature Encyclopedia of Life Sciences.

Shpak, M. and S.R. Proulx. 2007. The influence of life cycle and migration on selection for variance in the number of offspring. Bulletin of Mathematical Biology 69: 837-60.

Shpak, M. 2007. Selection against demographic stochasticity in age structured populations. Genetics 177: 2181-2194.

Kreinovich, V. and M. Shpak. 2008. Aggregability: its importance in bioinformatics and evolutionary computations, algorithms, and computational complexity (in Computational Intelligence in Bioinformatics, A. Keleman, editor, Springer-Verlag).

Shpak, M. 2008. Macroevolution. (Encyclopedia of Ecology, S.E. Jorgensen, editor, Springer-Verlag).

Shpak, M. 2008. The units of natural selection. (Encyclopedia of Ecology, S.E. Jorgensen, editor, Springer-Verlag).

Shpak, M., J.R. Kugelman, A. Varela-Ramirez, and R.J. Aguilera. 2008. The phylogeny and evolution of deoxyribonuclease II: an enzyme essential for lysosomal DNA degradation. Molecular Phylogenetics and Evolution 47: 841-854.

Kreinovich, V. and M. Shpak. 2009. Computational aspects of aggregation in biological systems (in Applications of Computational Intelligence in Biology: Applications and Open Problems, T. Smolinski, editor, Springer-Verlag).

Hernandez, Y., M. Shpak, T.T. Duarte, T.L. Mendez, R.A. Moldonado, S. Rowchudhury, M.L. Rodriges, and S. Das. 2008. The novel role of sphingolipid synthesis genes in regulating giardial encystation. Infection and Immunity 76: 2939-2949.

M. Yichoy, E.S. Nakayasu, M. Shpak, et al. 2009. Lipidomic analysis reveals that phosphatidylglycerol and Phosphaditylethanolamine are two newly synthesized phospholipids in the evolutionarily basal protozoan Giardia lamblia. Biochemical and Molecular Parasitology 65: 167-178.

Moschopoulos, P.M., and M. Shpak. 2010. The distribution of family size under a time-homogeneous birth and death process. Communications in Statistics 39: 1761-1775.

Shpak, M., J. Wakeley, D. Garrigan, and R.C. Lewontin. 2010. The coalescent in seasonally fluctuating structured populations. Evolution 64: 1395-1409.

Sreedharan, V. and M. Shpak. 2010. Selection for male-enforced uniparental inheritance of mitochondria. Theory in Biosciences 129: 295-306.

Shpak, M. 2012. Adaptive Landscapes. Pp. 17-26 in Sourcebook of Theoretical Ecology, University of California Press, eds. A. Hastings and L. Gross.

Shpak, M., S.H. Orzack, and E. Barany. 2013. The influence of demographic stochasticity on evolutionary dynamics and stability. Theoretical Population Biology 88: 47-56.

Shpak, M., M.M. Goldberg, and M.C. Cowperthwaite 2014. Cilia gene expression patterns in cancer. Cancer Genomics and Proteomics 11:13-24.

Shpak, M., G. Girotto-Gentil, and M. Miranda-Arango 2014. The origin and evolution of vertebrate glycine transporters. Journal of Molecular Evolution 78: 188-193.

Shpak, M., A. Weber Hall, M.M. Goldberg, D.Z. Derryberry, Y. Ni, V. Iyer, and M.C. Cowperthwaite 2014. An eQTL analysis of glioblastoma multiforme. Genomics 103: 252-263.

Shpak, M., M.M. Goldberg, and M.C. Cowperthwaite 2015. Rapid and convergent evolution in the Glioblastoma multiforme genome. Genomics 105: 159-167.

Hong, W.S., M. Shpak, and J.P. Townsend 2015. Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Research 75(19):4021-4025.

Beccar-Verela M.P., F. Biney, M.C. Marini, I. SenGupta, M. Shpak, and P. Bezdek 2016. Analysis of generic diversity in the fossil record, earthquake series, and high frequency financial data. In Florescu I, M.C. Marinia, H.E. Stanely, and F.G. Vienes. Handbook of High-Frequency Trading and Modeling in Finance. Wiley, New York NY.

Lu, J, M.C. Cowperthwaite, M.G. Burnett and M. Shpak 2016. Molecular predictors of long-term survival in Glioblastoma multiforme patients. PLOS One 111(4):e0154313.

Shpak, M. and J. Lu 2016. An evolutionary genetic perspective on cancer biology. Annual Review of Ecology, Evolution and Systematics 47: 25-49.

Lu, J, M.G. Burnett, and M. Shpak 2016. A comparative study of the molecular characteristics of familial gliomas and other cancers. Cancer Genomics and Proteomics 13: 467-474.

Shpak M, Y. Ni, J. Lu, and P. Mueller 2017. The variance in estimated genetic distance under different sampling models. Theoretical Population Biology 117: 51-63.

Weber Hall, A., A.M. Battenhouse, H. Shivram, M.C. Cowperthwaite, M. Shpak, and V. Iyer 2018. The epigenetic landscape of glioblastoma multiforme: common bivalent domains are strongly enriched for homeobox genes. Cancer Research 78: 2463-2474.

Shpak M., A. Ramakrishnan, M.C. Cowperthwaite, Z. Nadasdy, and C. Fanale 2018. Higher incidence of ischemic stroke in patients taking novel oral anticoagulants. Stroke 49: 2851-2856.

Shpak M., K. Korwek, Z. Nadasdy, A. Ramakrishnan, M.C. Cowperthwaite, K. Ankrom, J. Jennings et al 2019. Driving stroke quality improvement at scale in emergency departments across a nation-wide network of hospitals: strategies and interventions. Emergency Medicine Journal 36: 423-430.

Theofilatos K, A. Korfiati, S. Mavroudi, M.C. Cowperthwaite, and M. Shpak 2019. Discovery of stroke-related blood biomarkers from gene expression network models BMC Medical Genomics 12: 118.

Kennedy A, D. Shipley, M. Shpak, D. Moorman, L. Blakely, B. Hemphill et al 2019. Regorafenib prior to selective internal radiation therapy using Y90-resin microspheres for refractory metastatic colorectal cancer liver metastases: analysis of safety, dosimetry, and molecular markers Frontiers in Oncology 9: 624.

Ni Y., P. Mueller, M. Shpak, and Y. Ji 2019 Parallel-tempered feature allocation for large-scale tumor heterogeneity with deep sequencing data.Pp 233-248 in Liu and Tsong, Pharmaceutical Statistics, Springer New York NY.